CNV

1 Copy Number Analysis

1.1 CINdex amplification

1.2 CINdex deletions

1.2.1 CINdex Amplifications/Deletions only tumor

1.3 CINdex boxplots

1.4 CIN personalized method.

1.5 Gene level CNV

Downloading the Gene level Copy number files from TCGA, I computed CIN in the following way: - gene CNV > 2.25 = Amp - gene CNV < 1.75 = Del

Linear regression was applies using the R package limma (@limma).

1.6 HRD genes gene level CNV

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